Genome-Wide Identification and Characterization of the SBT Gene Family in maize and Its Expression in the Various tissue

doi:10.21203/rs.3.rs-3135702/v1

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Genome-Wide Identification and Characterization of the SBT Gene Family in maize and Its Expression in the Various tissue

https://doi.org/10.21203/rs.3.rs-3135702/v1

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published 27 Nov, 2023

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Maize is one of the three major crops in China. And SBT (Bacillus subtilis protease like serine protease) is a serine proteolytic enzyme, which widely exists in various organisms and participates in biological growth and defense. Therefore, it is necessary to study the SBT gene of maize. In this study, we identified 59 maize SBT genes (ZmSBTs), which were divided into 6 subfamilies through phylogenetic trees and distributed unevenly on 10 chromosomes. Analysis of cis-acting elements showed that ZmSBTs contained elements for plant growth and defense. In addition, the expression pattern of transcriptome data of different maize tissues shows that different ZmSBTs are expressed differently in different tissues. We also predicted the interaction of ZmSBT1.7and ZmSBT2.5 specifically expressed in meiosis_tassels with other maize proteins through the protein interaction website, and the interaction of ZmSBT1.2specifically expressed in seeds with other maize proteins. This study provided valuable information about maize SBT gene and clarified the possible biological functions of ZmSBT1.7, ZmSBT2.5 and ZmSBT1.2.

Proteolysis is the basis for normal life activities of multicellular organisms, and plays an important role in life processes such as growth and development, as well as defense and stress response to adapt to changing environments (Antão and Malcata, 2005; Von Groll et al., 2002). Serine proteases are a class of proteolytic enzymes with serine as the active center. Currently, there are three main types of plant serine proteases: subti lisin-like proteases (Subtilases), Clp proteases (Caseinolyticprotease) and Kexin-type protease (Duan et al., 2016; Ksiazek et al., 2015; Meyer et al., 2016). Among them, the genes encoding subtilisin-like proteases belong to the SBT family. In recent years, more and more studies have shown that Subtilases play an important role in immune stimulation in the interaction between plants and pathogens (Figueiredo et al., 2014). The study of the SBT gene family in plants is also increasing, such as Arabidopsis (Tripathi and Sowdhamini, 2006), Vitis vinifera (Cao et al., 2014) and tomato (Rose et al., 2010).

The most important feature of subtilases is that they have a catalytic triplet composed of aspartic acid (Asp), histidine (His) and serine (Ser) (Dodson and Wlodawer, 1998; Siezen and Leunissen, 1997). According to the MEROPS database classification (Rawlings et al., 2010), Subtilases belong to the S8 peptidase family. Subtilases are mainly divided into two subfamilies: Kexins and Pyrolysins, Most of the genes encoding subtilases in animals belong to the Kexins subfamily, while the SBT genes in plants basically belong to the Pyrolysins subfamily (Antão and Malcata, 2005). The Pyrolysins subfamily of most plant subtilases generally contains a signal peptide, propeptide domain (also known as the I9 inhibitory region), subtilisin domain (also known as the S8 peptidase domain), and a protease-associated domain (PA)(Vartapetian et al., 2011).

To date, the purification and functions of Subtilases in many different plants have been identified. As more and more plant genomes were deciphered, SBT genes in plants were also identified. The most common model plants, Arabidopsis and rice, contain 56 and 63 SBT gene members, respectively (Rautengarten et al., 2005; Tripathi and Sowdhamini, 2006), while the black poplar tree contains up to 90 subtilases genes (Schaller et al., 2012) The SBT gene in plants is not only abundant, but also widely involved in physiological activities and cellular activities. In Arabidopsis, SDD1 acts as a subtilisin-like serine protease involved in the mediation of a signal that regulate the density and distribution of stomata on the upper epidermis of leaves (Berger and Altmann, 2000). In AtSBT2.4 defective plant, the disrupted expression of AtSBT2.4 leads to defects in leaf shape formation and embryo development (Creff et al., 2019). Mutant seeds carrying loss-of-function alleles of AtSBT1.7 do not release mucilage upon hydration, affect the development or maturation of seeds (A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats). Moreover, SBT family gene also involve in senescence, programmed cell death (Coffeen and Wolpert, 2004; Fernández et al., 2015; Roberts et al., 2011).

Plants live in this complex world, and they often face some threats, such as the harm of pathogens. In order to adapt to the surrounding environment, plants often take some measures to prevent and eliminate the invasion of pathogens(Johansson, 2015). Gmsubpep, a short peptide in soybean leaves, belongs to the SBT family and can induce the expression of defense related genes CYP93A1, chib-1b, pdr12 and ACHS, resulting in the timely stimulation of defense signal pathway in Soybean after being attacked by pathogens (Pearce et al., 2010; Yamaguchi et al., 2011, p. 914). Overexpression of SBT3.3 of Arabidopsis subtilases gene can activate downstream immune signal transmission and induce innate immune response in Arabidopsis (Ramírez et al., 2013). When tomato is attacked by the pathogen Pseudomonas syringae, tomato will activate SA pathway, which induces the expression of two subilases, P69b and P69c (Jordá et al., 1999; Tornero et al., 1997). Moreover, subsequent studies found that tomato cell death was inhibited when p69b was silenced, which showed that subtilases acted on the extracellular proteolysis cascade and helped regulate tomato cell death (Zimmermann et al., 2016).

Maize (Zea mays) belongs to the family of Poaceae, it is not only one of the three most important food crops in the world, but also is an important source of feed and industrial raw materials. Among them, the important factor affecting the yield of maize is the development of endosperm, which is the main storage organ of maize seeds, is essential for seed development, and provides nutrition for seedlings during germination. In 2017, Maribel and his colleagues found that SBT1 (Zea mays Subtilisin1) is expressed at the developing aleurone in a time-regulated manner, while SBT2 concentrates at the pedicel in front of the endosperm basal transfer layer, that affect the development of maize endosperm (López et al., 2017, p. 2). Although the function of a small part of SBT gene in maize has been determined, it is of great significance to carry out basic research on SBT gene family in maize due to the versatility of SBT gene. In this study, ZmSBTs gene was identified by bioinformatics methods. based on phylogenetic analysis, it can be found that it is mainly divided into six subfamilies, and then Characterize them by gene distribution in chromosome, primary structure of gene and protein, and RNA-seq expression profile, to understand the impact of ZmSBTs gene on maize yield.

Materials

Maize genome data from maize database (https://qteller.maizegdb.org/). The SBT amino acid sequences of Oryza sativa, Arabidopsis thaliana (Tripathi and Sowdhamini, 2006), Ananas comosus (Jin et al., 2021) and Solanum tuberosum (Norero et al., 2016) were obtained from published literature.

Prediction and characterization of SBT in maize and Euclaena mexicana

From Pfam Protein Family Database (http://pfam.xfam.org/) Download Peptidase_ The hidden Markov model (HMM) of S8 domain (PF00082) (Finn et al., 2014), HMM search program (HMMER3.0) is applied to the downloaded maize protein database, and the hmmbuild is used to build the basis of the HMM map (Potter et al., 2018). Then hmmsearch is used to identify the ZmSBT protein in the genome, and the results are combined to remove redundant sequences. Check the ZmSBT domain through the CDD search function of NCBI (Marchler-Bauer et al., 2010) and pfam, and manually exclude the sequences that are missing or contain incomplete ZmSBT domains. Using ExPASy (Duvaud et al., 2021) ProtParam (Sigrist et al., 2002) to calculate the basic physical and chemical properties of maize ZmSBT protein (http://web.expasy.org/protparam/), including amino acid number (NA), molecular weight (MW), theoretical PI value, total average hydrophilicity (GRVAY), lipolysis index (AI) and instability coefficient (II). After that, TMHMM (Krogh et al., 2001) (http://www.cbs.dtu.dk/services/TMHMM/) signal (Emanuelsson et al., 2007) and WoLF PSORT (Horton et al., 2007) were used to predict transmembrane, signal peptide and subcellular localization, respectively.

Sequence alignment and construction of a geophysical tree of ZmSBT

The identified ZmSBT protein sequence was multiple compared with pineapple SBT through mafft (Katoh et al., 2002), and the default parameter auto was used for correction. Then use IQ-Tree (Minh et al., 2020, p. 2) to build the phylogenetic tree. Here, 1000 repeated Bootstrap tests are performed. Group according to pineapple AcoSBT’s group scheme. Finally, use Evoview (Subramanian et al., 2019, p. 3) to visualize the evolution tree.

Gene structure, motif analysis and conservative domain analysis of ZmSBT

Based on the GFF file of maize, TBtool (Chen et al., 2018) software is used to analyze the gene structure of the given maize SBT gene family members, showing the basic structural characteristics of the gene and the relevant tissues of exon-intron. Use the MEME (Granziol et al., 2019) tool program on the Galaxy web platform to analyze motifs of ZmSBT, Parameters: motif width < 50, motif = 10, e-value < e^− 5. Submit the maize SBT protein sequence to the CDD-search module in NCBI to obtain the conservative domain.

Chromosome distribution, gene duplication events and selection pressure analysis

Obtain the specific location information of ZmSBT genes from the maize genome data, including the starting position, the length of the chromosome where it is located, and the chromosome number where it is located, and finally use Mapchart (Voorrips, 2002) for visualization. Two genes belonging to the same ZmSBT family are separated by less than 10 genes on the same chromosome and are considered to be consecutive duplicates (Wei and Chen, 2018). The BLASTP with e^− value<e ^− 5 was used to search for potential anchor points between maize and Euclaena mexicana, and the first five matches were screened. these duplicate gene pairs were visualized by Circos (Krzywinski et al., 2009). The date of occurrence of the duplication event of the gene pair was calculated according to the formula T = Ks/2λ × 10^− 6Mya (λ = 6.5 × 10 − 9) (Lee et al., 2008).

Prediction of cis-acting elements, Construction of protein Interaction Network and Expression profile analysis of ZmSBT in different organs

A sequence 2000 bp upstream of the ZmSBT promoter translation start codon was extracted from the rice genome sequence using a BioPerl custom script, and potential cis-acting elements were predicted at PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) (Lescot et al., 2002). The ZmSBT proteins interaction network was examined using the STRING online server (https://string-db.org/cgiaccessed on 15 May 2021) (Szklarczyk et al., 2015). To further understand the response of ZmSBT gene expression in different development stages. The expression amount of 9 different organs of maize, including root, stem and leaf, was obtained from the article reported by Scott in 2015. The heat map is generated using TBtool software.

Identification and Characterization of Subtilisin-Like Serine Protease Genes in maize

The genome message was downloaded through the maize database. In order to identify SBTs in maize, we use the Hidden Markov Model (HMM) tool to search all the possible SBTs on maize peptide maizegdb (Version 3.22) with Peptidase_S8 domain (PF00082) as the query. Then, the batch CD-search of NCBI was employed to ensure that all the identified sequences contain the target domain, such as Peptidase_S8 domain. etc (Marchler-Bauer et al., 2011). Finally, we identified 59 ZmSBTs in Z.mays and give them name according to their phylogenetic relationships with pineapple's SBT proteins (Supplementary Table S1). Then the basic physical and chemical properties of the 59 ZmSBTs were evaluated in Supplementary Table S2, including coding sequence (CDS) lengths, protein lengths, isoelectric point, and molecular weight. The coding sequence of ZmSBTs have 259 ~ 1040 amino acids, but most of the sequences have 700 ~ 800aa in length. The molecular weight ranged from 28.05 and 115.61 kDa, but most of them are between 75.00 and 85.00. The range of isoelectric points of these 59 ZmSBT genes varies greatly, ranging from 4.68 to 9.60, of which 31 genes have isoelectric points less than 7.0. The span of these characteristics is relatively large, which indicates that the biochemical characteristics of ZmSBT are diverse. The instability index gives us a message of whether ZmSBT is stable or unstable in various biochemical processes. Table S2 shows that ZmSBT is relatively stable and about two-thirds are hydrophilic proteins.

In order to determine the molecular function of ZmSBT, we predicted the subcellular localization through WoLF PSORT, the results of subcellular localization predicted that ZmSBT was widely localized, almost half of ZmSBT was located in chloroplast, and the rest were located in vacuole, plasma membrane, Peroxisomes, nucleus, mitochondrion, Extracell and Cycloplast respectively. There is only one ZmSBT protein located in Peroxisomes and nucleus, ZmSBT5.4 and ZmSBT2.2. At the same time, we also predicted that ZmSBT3.3 located not only in chloroplast, but also in mitochondrion.

Phylogenetic Analysis of maize SBTs

The phylogenetic tree of pineapple and maize SBT family was constructed using the neighbor joining statistical method. According to previously reported, 59 ZmSBT genes were divided into 6 subfamilies, namely Group I, Group II, Group III, Group IV, Group V, and Group VI. The largest subfamily is Group I, with a total of 30, and the smallest subfamily is Group VI, just 2 genes (Fig. 1A).

To further understand the characteristics of SBT family in monocotyledons and dicotyledons, Euclaena mexicana, Oryza sativa, Arabidopsis thaliana, Ananas comosus, Zea mays and Solanum tuberosum were selected for evolutionary tree analysis and the results revealed that there were most SBT genes in potato genome than other, and the teosinte SBT gene are the least (Fig. 1B and Supplementary Table S3). Through the quantitative analysis of the SBT family genes of these six species, an interesting phenomenon was found, In monocotyledons, the number of group Ⅰ is the largest, while group Ⅳ is the least. But in dicotyledons, on the contrary, group Ⅳ is the most and group Ⅰ is the least. The interesting phenomenon is that the number of group VI family is not much different in monocotyledons or dicotyledons which shows that group VI is conservative.

Gene Structure Characterization and protein Motif Identification

Gene structure often determines gene function, so understanding the diversity of gene structure helps to understand gene function. In order to further understand the gene structure of zmSBT, exon-intron organization of ZmSBT genes are analyzed by TBtools. As shown in Fig. 2, the gene structure of the same subgroup tends to be more similar. The gene structure of group I is simple, often contains only one exon, and the gene length is also highly conservative, except for ZmSBT1.30 and ZmSBT1.17. While the gene structure of other subgroups is relatively complex, including 3 or more exons, however, the ZmSBT5.1 gene only contains one exon, which is different from the gene structure in the fifth group. This may be caused by the loss of the remaining exons of the ZmSBT5.1 gene during evolution. (Fig. 2B)

Protein motifs represent the necessary part of the conserved binding sites or catalytic sites retained in the evolution of the same ancestral protein family. Different proteins may have the same or similar functions if they contain the same structural motifs. Therefore, in order to understand the functional diversity of proteins, the conserved and diversified motifs were further identified by meme with setting 10 motifs (Fig. 2A). Motif 7 is present in almost all ZmSBTs except AcoSBT2.2 and AcoSBT2.6. The fifth group gene all contains 10 motifs. The conserved motif of group III gene is 2-6-7-4-3. and the conserved motif of group IV gene is 9-10-2-6-7-4. Except ZmSBT1.11 and ZmSBT1.29, all group I contains these 10 motifs.

There are three conserved domains in the SBT gene family, peptidase S8, PA peptide and inhibitor I9 peptide (Fig. 2C). Except ZmSBT3.4, ZmSBT4.1, ZmSBT4.3, ZmSBT6.2, ZmSBT2.1, ZmSBT2.6 and ZmSBT2.2, other genes all contain peptidase S8. Almost all ZmSBT genes contain PA peptides for substrate recognition, except for group VI and some group II genes (ZmSBT2.6 and ZmSBT2.2).

Chromosome location and evolutionary analyses of ZmSBTs

There are 10 chromosomes in the maize genome, and 59 ZmSBTs are unequally distributed on these 10 chromosomes. As shown in Addition figure S3, the fourth chromosome contains the smallest number of ZmSBTs, only 2, while Chr1 contains the most ZmSBTs, up to 11.

To further investigate the evolutionary mechanisms of the ZmSBT family, all intragenomic and intergenomic duplication data files of maize were filtered by MCScan, just 4 pairs of duplicated genes were found, ZmSBT2.7/ZmSBT2.5, ZmSBT1.2/ZmSBT1.15, ZmSBT1.18/ZmSBT1.28 and ZmSBT1.2/ZmSBT1.29(Fig. 3 and Supplementary Table S4). Obviously, these four pairs of gene duplication occur in the same group, so it can be seen that each subgroup is quite conservative. Group I subfamily has more replication events than other families, indicating that they play an important role in SBT amplification in Maize. There are two main types of gene replication. Segmental replication and tandem segment replication are long and almost identical DNA fragments, which belong to gene duplication in specific regions of chromosomes. Repetitions range from one chromosome to the whole genome. It is usually the most common in plants, so a large number of duplicate chromosome blocks are retained in their genomes (Yu et al., 2005). Tandem replication mainly occurs in the chromosome recombination region (Li et al., 2001). The gene family members generated by tandem replication are usually closely arranged on the same chromosome, forming gene clusters with similar sequences and functions (Holub, 2001). These four pairs of genes belong to segment duplication, which indicates that segment duplication contributes greatly to the expansion of ZmSBT gene family.

Euclaena mexicana is the ancestor of maize. In order to understand the evolutionary mechanism between them, we further conducted collinearity analysis of ZmSBT between teosinte and maize. A total of 28 homologous genes were identified, indicating that these genes are very conservative and have existed in an earlier period. We also found some interesting phenomena, such as the collinearity of one gene in teosinte corresponding to two genes in maize, such as EmSBT1.10-ZmSBT1.2/ZmSBT1.15, EmSBT1.2-ZmSBT1.18/ZmSBT1.28, EmSBT2.1-ZmSBT2.8/ZmSBT2.6, EmSBT2.2-ZmSBT2.8/ZmSBT2.6, EmSBT2.3-ZmSBT2.7/ZmSBT2.5 and EmSBT3.2-ZmSBT3.6/ZmSBT3.13, these genes may be formed after the differentiation of teosinte and maize. Similarly, these 28 gene pairs all occur in the same group, which indicates that the ZmSBT family genes are very conserved in the evolution process. We further calculated the Ka/Ks values of the gene pairs shown on the comparative synteny map (Supplementary Table 3), we found that the Ka/Ks value of all gene pairs is less than 1, when the Ka/Ks value is less than 1, it means that they are experiencing negative selection. Among these gene pairs, the EmSBT1.8/ZmSBT1.6 pair has the highest Ka/KS, up to 0.93. These results indicate that the SBT family genes in maize have experienced strong intensified selection pressure.

In order to understand the evolutionary relationship between the maize SBT gene and the SBT gene of dicotyledonous and monocotyledonous plants, we conducted collinearity analysis with the maize SBT gene and the monocotyledonous representative plants rice and teosinte, the dicotyledonous representative plants Arabidopsis and potato, respectively. According to the syntenic analyze results (Addition Figure S4), in monocotyledonous, there are 42 orthologous gene pairs in maize and teosinte and 40 orthologous gene pairs in maize and rice. However, there are only three orthologous gene pairs of Arabidopsis and potato.

Cis-Acting Elements Identification in Promoter Region of ZmSBTs

In order to further understand the biological role of ZmSBT gene in maize, we intercepted the 2000bp upstream of all ZmSBT genes to predict its potential cis-acting element. In addition to the common TATA box, CAAT box and some unknown elements, a total of 1441 cis-acting elements of 27 types were identified (Supplementary table S5). It is mainly divided into plant growth and development response elements, stress-related response elements and plant hormone related response elements. Among them, growth and development response elements mainly include AE box, ACE, ATCT motif, I-box, box-4, G-box and GATA motif. Box-4 has the largest number, up to 71, followed by G-box and GATA motif. This indicates that these three cis-acting elements play a very important role in the growth and development of ZmSBT on maize. Similarly, the representative elements of stress related response elements include ABRE, ARE, DRE1, ERE, LTR and STR, among which the highest number is abre elements, up to 293.

According to the analysis of cis-regulatory elements of ZmSBT genes, the binding sites of key transcription factors are related to phythohormone response elements (43%), stress related elements (36%) and growth response and development elements (21%) (Fig. 4 and Supplementary Table S5). At the same time, various hormones such as auxin, salicylic acid, abscisic acid, gibberellin and methyl jasmonate (MeJA) were also found. Besides, In order to understand the correlation between each subgroup and cis-acting elements, we analyzed the cis-acting elements of each subgroup (Fig. 4). We found that not all groups contain these 27 cis-acting elements, for example, group IV and group VI do not contain ACE elements and AE boxes, while ATC and ATCT motif elements are only contain by group I ~ III. However, the distribution of cis-acting elements in the promoter region has no strong correlation with phylogenetic groups.

Spatio-T emporal Expression Profiles of AcoSBTs in maize

As an initial step towards understanding of the biological function, the expression patterns of ZmSBTs during entire growth and developmental cycle analyzed using available oligonucleotide microarray data is necessary. We used the transcriptome data published by Scott C.(Stelpflug et al., 2016) on original research to analyze the expression profiles of all SBT genes in different tissues and development stages. Understanding the expression of 59 ZmSBTs in various tissues of maize will help to understand the difference in the role of ZmSBT genes in different tissues of maize, so as to predict their potential functions (Supplementary Table 6). As shown in Fig. 5, ZmSBT’s expression is different in various tissue. ZmSBT1.22 and ZmSBT5.4 show highly expression in leaf. Seven genes, including ZmSBT5.10, ZmSBT2.3, ZmSBT1.7, ZmSBT1.21, ZmSBT5.3, ZmSBT1.20 and ZmSBT5.1, have highly transcript level during meiotic tassel development in maize, while they are show low expression in other tissues. Therefore, these genes play a vital role in tassel development in maize. And we also found an interesting phenomenon. Some ZmSBT are expressed in all tissues, and its wide expression shows that it is essential for the growth, development and reproduction of maize, sucn as ZmSBT1.9, ZmSBT6.1, ZmSBT2.2. In group IV, almost all genes were poorly expressed in all tested samples, which indicates that this group of genes may not play a role in the development of maize. In addition, there are also some genes of group I that do not participate in the development of maize, such as ZmSBT1.22, ZmSBT1.29, ZmSBT1.11 and ZmSBT1.14. Although the number of genes in group I is the largest, there are also some genes that do not function, which may be due to the loss of their original role during evolution.

Protein-Protein Networks Analysis of the ZmSBT Family Genes

To understand the interaction of ZmSBT with other proteins and better understand its potential function, we constructed a network using the STRING database (Fig. 6 and Supplementary Table S7). According to the predicted results, We identified two ZmSBT proteins specifically expressed in meiotic tassel tissues to interact with 8 and 5 different proteins in maize, respectively. ZmSBT1.7 interacts with GRMZM5G891373_P02, GRMZM5G803365_P01, GRMZM2G167338_P01, GRMZM2G077034_P01 and GRMZM5G895188_P02, while ZmSBT2.5 interacts with Oleosin Zm II, GRMZM2G108894_P01, GRMZM2G380650_P02, GRMZM2G477683_P01, GRMZM2G060481_P01, GRMZM2G447984_P01, GRMZM2G056231_P01 and GRMZM2G143373_P01. In addition, we also identified the interaction between the specific expression of ZmSBT protein in roots and seeds, and other proteins in maize. ZmSBT1.25, specifically expressed in maize roots, can interact with GRMZM5G866861_P02, GRMZM2G335978_P01, GRMZM2G119397_P01, GRMZM5G831795_P03, GRMZM2G098583_P01, GRMZM2G168115_P01 and GRMZM2G13. And ZmSBT1.25, specifically expressed in maize seeds, can interact with GRMZM2G167338_P01, GRMZM2G008327_P01, GRMZM5G878541_P02, GRMZM2G421491_P01, GRMZM2G092174_P01, GRMZM2G077034_P01, GRMZM2G103647_P01, GRMZM2G029979_P01, GRMZM5G803365_P01 and GRMZM5G891373_P02.

SBT family is a family with a wide range of functions. It not only participates in plant growth and development, but also participates in plant abiotic stress response. For example, One SBT gene can produce a relatively large amount of secondary vascular tissue in the root hypocotyl of Arabidopsis thaliana (Zhao et al., 2000). According to the reports, SBT is also involved in the development of air roots and plant epidermis (Neuteboom et al., 1999), thus participating in the growth and development of plants (Riggs et al., 2001). In Arabidopsis thaliana, SDD1 ,a gene of SBT family, as a processing protease, it is involved in regulating signals and controlling the development of cell lineages that lead to the formation of protective cells (Berger and Altmann, 2000). CsKPI, a Kazal type serine proteinase inhibitor, plays an important role in innate immunity in tomato(Tian et al., 2004). Arabidopsis subtilise (SBT3.3) was confirmed to be a receptor located in the plasma membrane, activating the downstream immune signaling process and initiating the immune system of Arabidopsis (An extracellular subtilases switch for immune priming in Arabidopsis).

In this study, we identified 59 ZmSBT in the genome of Maize by HMM, which is similar to that of A.thaliana and teosinte, but 38.9% less than that of potato. This may be because ZmSBT is undergoing this evolutionary selection and has lost some genes in the process of evolution. In order to reveal the genetic relationship of SBTs, a phylogenetic tree was constructed, and it show that ZmSBT was mainly divided into six groups, of which group Ⅰ is the largest, accounting for 50.8%, while group Ⅵ had the smallest number, only containing two genes (Fig. 1). Compared with the phylogenetic tree of Euclaena mexicana, Oryza sativa, A.thaliana, Ananas comosus, Zea mays and Solanum tuberosum, it was found that the content of group Ⅰ was the highest in monocotyledons, while that of group Ⅳ was the lowest, while that of dicotyledons was the opposite.

In the subsequent analysis of gene structure and motif analysis (Fig. 2), it was found that group Ⅰ contained almost no exons, and group Ⅱ had the most complex gene structure. The gene structure and motif composition of each group were very similar, but there were obvious differences between groups. These results indicate that each group of SBT has different functions. Analysis of gene replication events shows that gene replication in SBT families generally occurs in the same group and 75% of genes belong to group Ⅰ (Fig. 3 and Addition Figure S4).

For a long time, the male inflorescence has been used as an important morphological structure for taxonomic comparison between maize and teosinte (Doebley et al., 1990). Since domestication, the tassel has undergone tremendous changes. Watson found that the size of the male spike is related to the maize grain yield (Doebley, 1983). Subsequent experiments further showed that smaller male spikes can improve the maize grain weight and production efficiency (Genetic progress in yield of United States maize). Previous studies have shown that SBT gene will participate in anther formation, the subtilase gene AcoSBT1.8 enriched during the development of ovule and stamen, related to the development of petals (Wang et al., 2020). And the expression analysis of SBT family genes during maize development showed that ZmSBT1.7 and ZmSBT2.3 were specifically expressed in maize Meiosis-tassels. And ZmSBT1.7 and AcoSBT1.8 are closely related in phylogenetic trees. Therefore, we We have reason to believe that the function of ZmSBT1.7 is similar to the AcoSBT1.8, they are playing an important role in the meiotic stage of tassels. At the same time, the string database reveals that ZmSBT2.5 can interact with 8 different proteins in maize, three of which belong to the chalcone/stilbene synthases family and are Type III polyketide synthase (GRMZM2G108894_P01, GRMZM2G380650_P02 and GRMZM2G477683_P01) (Fig. 6 and Supplementary Table S7). Plant type III PKS enzymes are related to the synthesis of some antifungal substances, such as glucoside compounds and their derivatives of chrysanthemum (Eckermann et al., 1998; Helariutta et al., 1995), bibenzyl stilbenes and their tricyclic derivatives, 9,10-dihydrophenanthrenes of orchid (Gehlert and Kindl, 1991; Preisigmuller et al., 1995; Reinecke and Kindl, 1993), pinosylvin of pine (Schanz et al., 1992), and xanthone of hypericum (El-Mawla et al., 2002) can resist bacteria and Fungal growth prevents insect feeding. In addition, previous studies have shown that it is also related to the development of anthers and may be related to the biosynthesis of pollen cell walls (Atanassov et al., 1998; Burbulis et al., 1996; Ylstra et al., 1996). Therefore, we speculate that ZmSBT2.5 may be involved in the synthesis of maize anther and the production of antifungal substances together with the proteins of the chalcone/stilbene synthases family. In addition, the ZmSBT2.5 protein also can interact with two histones, GRMZM2G447984_P01 and GRMZM2G056231_P01. They belong to nucleosomal histone families, H3 and H2A, respectively (Fig. 6 and Supplementary Table S7). During plant meiosis, histones play a crucial role, and the histone H3 family specifically phosphorylates histones in a particularly spatially and temporally coordinated pattern during meiosis (Ingouff and Berger, 2010). And H2AZ appears to alter nucleosome stability, is partially redundant with the nucleosome remodeling complex, and is involved in transcriptional control (Redon et al., 2002). These results suggest that ZmSBT2.5 interacts with proteins from nucleosomal histone families involved in maize tassel meiosis. ZmSBT1.7 also specifically expressed in meiotic-tassel (Fig. 5 and Supplementary Table S6). Through the display of string database, ZmSBT1.7 cooperates with other maize proteins to participate in tassel meiosis. such as GRMZM5G895188_P02, a β-glucosidase that degrades the glycosphingolipid glucosylceramide (GlcCer) into glucose and ceramide, loss of GBA2 function leads to accumulation of GlcCer and dysregulation of lipid homeostasis (Raju et al., 2015; Schonauer et al., 2017), GRMZM2G167338_P01 (a telomerase reverse transcriptase catalytic subunit variant), and GRMZM5G891373_P02 (Belonging to the class-I aminoacyl-tRNA synthetase family). As this study show that ZmSBT1.7 and ZmSBT2.5 are indispensable in the meiotic phase of the tassel.

ZmSBT1.2 was specifically expressed in seeds, and the expression level was very high (Fig. 5). The string diagram shows that ZmSBT1.2 interacts with other maize proteins and plays a role in metabolic process of seed, such as GRMZM2G421491_P01 (a glutathione transporter), GRMZM2G008327_P01(a cell division control protein 2 homolog, belonging to the protein kinase superfamily), GRMZM5G891373_P02 (Glutamate–tRNA ligase chloroplastic/mitochondrial; Belongs to the class-I aminoacyl-tRNA synthetase family) (Fig. 6 and Supplementary Table S7). In addition, ZmSBT1.2 can also interact with Gibberellin-regulated protein (GRMZM2G077034_P01), while gibberellin is an important plant growth regulator, which can relieve seed dormancy and promote germination (White et al., 2000; Yamaguchi et al., 2014). Therefore, we speculate that ZmSBT1.2 may be involved in seed germination. Light plays a very important role in the development of corn seeds, and it can affect the young plant emerging from the seed. When the light is limited, plants fade; hypocotyl grows and the leave growth stops. When plants are exposed to light, hypocotyl growth stops and a normal growth starts in epicotyl (Mirmostafaee et al., 2020). Phytochromes are photoreceptors that absorb red and far-red light and are used by plants to sense light to distinguish day from night, And related to the germination of plant seeds (Aukerman et al., 1997; Bewley and Black, 2012). ZmSBT1.2 can interact with Phytochrome GRMZM2G092174_P01 and participate in the germination of maize seeds. In conclusion, ZmSBT1.2 gene may be involved in maize seed development and germination.

Previous studies have shown that the gene function of group Ⅰ is quite extensive, and it can participate in the growth and development of plants. In Arabidopsis, AtSBT1.7 negatively regulates the activity of pectin methylesterase (PME) at the late stage of seed development, reduces demethylation and esterification of seed mucus, and increases its germination rate under low water conditions (Rautengarten et al., 2008). In the expression profile (Fig. 5 and Supplementary Table S6), the expression of ZmSBT1.4 increased dramatically in the middle and late stages of maize whole-seed development, which may negatively regulate PME activity to ensure germination of maize. In Arabidopsis, AtSBT1.1 can participate in the maturation of plant Thioflavin (PSK), promote cell division of root tip meristem and regulate immune response (Matsubayashi and Sakagami, 1996). In maize, ZmSBT1.25, ZmSBT1.13 and ZmSBT1.31 have high expression in roots, but low expression in other tissues. They maybe participate in the maturation of PSK, but whether these genes are related to root elongation needs further experimental verification. According to the expression pattern of ZmSBT, many genes show tissue specificity. For example, ZmSBT1.4 are specifically expressed in maize whole-seeds and Endosperm, it may like the SBT1.1 of peas endosperm that control the change of seed size by regulating embryonic cell division (D’erfurth et al., 2012). Through collinearity analysis, genome localization and expression profile analysis, it can be found that group Ⅰ not only has a large number, but also has obvious correlation with plant growth and development. These evidences prove that it is an indispensable subfamily in the SBT family.

In all ZmSBT, Most of the groups Ⅲ had low expression during maize breeding while group Ⅳ was not expressed in almost all tissues of maize (Fig. 5 and Supplementary Table S6). This phenomenon is consistent with the previously report—overexpression of AtSBT5.3 in Arabidopsis has longer lateral roots without changes in root density or cell wall abnormalities(Veth-Tello, 2005). And it can act downstream of the transcription factor NaCI to mediate auxin induced lateral root growth (Serrano et al., 2016). This indicates that groups Ⅲ mainly participates in the growth and development of vegetative organs.

In this study, we identified and analyzed the SBT gene family at the whole genome level of maize. A total of 59 ZmSBT genes were identified, which were divided into 6 groups. The gene structure and function between groups were quite different. subsequently, through the evolutionary scenario analysis with the SBT gene of dicotyledons and monocotyledons, it was found that ZmSBT was highly conservative. Through the expression profile analysis of ZmSBT, it was found that Group Ⅰ was widely involved in the growth and development and breed of maize, while Group Ⅲ and Group Ⅴ were mainly involved in the growth of maize, but did not seem to play a significant role in the reproduction of maize. At the same time, Group Ⅳ did not seem to participate in the whole growth and reproduction process of maize.

Acknowledgements

This work was supported by Research Program of science and technology at Universities of Inner Mongolia Autonomous Region (NJZY22463) and Open Fund Project of Key Laboratory of Ecological Agriculture in Horqin Sandy Land of State Civil Affairs Commission（MDK2021081）.

Author Contributions:

X.D.W. and Z.G.L. conceived this project and coordinated research activities; P.L. designed experiments; Y.T.Z and D.J.X did gene family analysis. Y.T.Z and X.D.W and M W wrote the manuscript, W.W.Z.revised the manuscript.

Competing financial interests:

The authors have no competing interests.

Additional information

Correspondence and request for materials should be addressed to X.D.W.

Antão, C.M., Malcata, F.X., 2005. Plant serine proteases: biochemical, physiological and molecular features. Plant Physiology and Biochemistry 43, 637–650.
Atanassov, I., Russinova, E., Antonov, L., Atanassov, A., 1998. Expression of an anther-specific chalcone synthase-like gene is correlated with uninucleate microspore development in Nicotiana sylvestris. Plant molecular biology 38, 1169–1178.
Aukerman, M.J., Hirschfeld, M., Wester, L., Weaver, M., Clack, T., Amasino, R.M., Sharrock, R.A., 1997. A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing. The Plant Cell 9, 1317–1326.
Berger, D., Altmann, T., 2000. A subtilisin-like serine protease involved in the regulation of stomatal density and distribution in Arabidopsis thaliana. Genes & development 14, 1119–1131.
Bewley, J.D., Black, M., 2012. Physiology and biochemistry of seeds in relation to germination: volume 2: viability, dormancy, and environmental control. Springer Science & Business Media.
Burbulis, I.E., Iacobucci, M., Shirley, B.W., 1996. A null mutation in the first enzyme of flavonoid biosynthesis does not affect male fertility in Arabidopsis. The Plant Cell 8, 1013–1025.
Cao, J., Han, X., Zhang, T., Yang, Y., Huang, J., Hu, X., 2014. Genome-wide and molecular evolution analysis of the subtilase gene family in Vitis vinifera. BMC genomics 15, 1–15.
Chen, C., Chen, H., He, Y., Xia, R., 2018. TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv 289660.
Coffeen, W.C., Wolpert, T.J., 2004. Purification and characterization of serine proteases that exhibit caspase-like activity and are associated with programmed cell death in Avena sativa. The Plant Cell 16, 857–873.
Creff, A., Brocard, L., Joubès, J., Taconnat, L., Doll, N.M., Marsollier, A.-C., Pascal, S., Galletti, R., Boeuf, S., Moussu, S., others, 2019. A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis. PLoS genetics 15, e1007847.
D’erfurth, I., Le Signor, C., Aubert, G., Sanchez, M., Vernoud, V., Darchy, B., Lherminier, J., Bourion, V., Bouteiller, N., Bendahmane, A., others, 2012. A role for an endosperm-localized subtilase in the control of seed size in legumes. New Phytologist 196, 738–751.
Dodson, G., Wlodawer, A., 1998. Catalytic triads and their relatives. Trends in biochemical sciences 23, 347–352.
Doebley, J., Stec, A., Wendel, J., Edwards, M., 1990. Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proceedings of the National Academy of Sciences 87, 9888–9892.
Doebley, J.F., 1983. The maize and teosinte male inflorescence: a numerical taxonomic study. Annals of the Missouri Botanical Garden 32–70.
Duan, X., Zhang, Z., Wang, J., Zuo, K., 2016. Characterization of a novel cotton subtilase gene GbSBT1 in response to extracellular stimulations and its role in Verticillium resistance. PLoS One 11, e0153988.
Duvaud, S., Gabella, C., Lisacek, F., Stockinger, H., Ioannidis, V., Durinx, C., 2021. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. Nucleic Acids Research.
Eckermann, S., Schröder, G., Schmidt, J., Strack, D., Edrada, R.A., Helariutta, Y., Elomaa, P., Kotilainen, M., Kilpeläinen, I., Proksch, P., others, 1998. New pathway to polyketides in plants. Nature 396, 387–390.
El-Mawla, A., Ahmed, M., Beerhues, L., 2002. Benzoic acid biosynthesis in cell cultures of Hypericum androsaemum. Planta 214, 727–733.
Emanuelsson, O., Brunak, S., Von Heijne, G., Nielsen, H., 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nature protocols 2, 953–971.
Fernández, M.B., Daleo, G.R., Guevara, M.G., 2015. Isolation and characterization of a Solanum tuberosum subtilisin-like protein with caspase-3 activity (StSBTc-3). Plant Physiology and Biochemistry 86, 137–146.
Figueiredo, A., Monteiro, F., Sebastiana, M., 2014. Subtilisin-like proteases in plant–pathogen recognition and immune priming: a perspective. Frontiers in plant science 5, 739.
Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Heger, A., Hetherington, K., Holm, L., Mistry, J., others, 2014. Pfam: the protein families database. Nucleic acids research 42, D222–D230.
Gehlert, R., Kindl, H., 1991. Induced formation of dihydrophenanthrenes and bibenzyl synthase upon destruction of orchid mycorrhiza. Phytochemistry 30, 457–460.
Granziol, D., Ru, B., Zohren, S., Dong, X., Osborne, M., Roberts, S., 2019. MEMe: An accurate maximum entropy method for efficient approximations in large-scale machine learning. Entropy 21, 551.
Helariutta, Y., Elomaa, P., Kotilainen, M., Griesbach, R.J., Schröder, J., Teeri, T.H., 1995. Chalcone synthase-like genes active during corolla development are differentially expressed and encode enzymes with different catalytic properties in Gerbera hybrida (Asteraceae). Plant Molecular Biology 28, 47–60.
Holub, E.B., 2001. The arms race is ancient history in Arabidopsis, the wildflower. Nature Reviews Genetics 2, 516–527.
Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C., Nakai, K., 2007. WoLF PSORT: protein localization predictor. Nucleic acids research 35, W585–W587.
Ingouff, M., Berger, F., 2010. Histone3 variants in plants. Chromosoma 119, 27–33.
Jin, X., Liu, Y., Hou, Z., Zhang, Y., Fang, Y., Huang, Y., Cai, H., Qin, Y., Cheng, Y., 2021. Genome-Wide Investigation of SBT Family Genes in Pineapple and Functional Analysis of AcoSBT1. 12 in Floral Transition. Frontiers in genetics 1466.
Johansson, O., 2015. Plant pathogen defense: Signalling, resistance and cell death.
Jordá, L., Coego, A., Conejero, V., Vera, P., 1999. A genomic cluster containing four differentially regulated subtilisin-like processing protease genes is in tomato plants. Journal of Biological Chemistry 274, 2360–2365.
Katoh, K., Misawa, K., Kuma, K., Miyata, T., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 3059–3066.
Krogh, A., Larsson, B., Von Heijne, G., Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology 305, 567–580.
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., Marra, M.A., 2009. Circos: an information aesthetic for comparative genomics. Genome research 19, 1639–1645.
Ksiazek, M., Karim, A.Y., Bryzek, D., Enghild, J.J., Thøgersen, I.B., Koziel, J., Potempa, J., 2015. Mirolase, a novel subtilisin-like serine protease from the periodontopathogen Tannerella forsythia. Biological chemistry 396, 261–275.
Lee, D.-S., Nioche, P., Hamberg, M., Raman, C., 2008. Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes. Nature 455, 363–368.
Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P., Rombauts, S., 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research 30, 325–327.
Li, X., Clarke, J.D., Zhang, Y., Dong, X., 2001. Activation of an EDS1-mediated R-gene pathway in the snc1 mutant leads to constitutive, NPR1-independent pathogen resistance. Molecular plant-microbe interactions 14, 1131–1139.
López, M., Gómez, E., Faye, C., Gerentes, D., Paul, W., Royo, J., Hueros, G., Muniz, L.M., 2017. zmsbt1 and zmsbt2, two new subtilisin-like serine proteases genes expressed in early maize kernel development. Planta 245, 409–424.
Marchler-Bauer, A., Lu, S., Anderson, J.B., Chitsaz, F., Derbyshire, M.K., DeWeese-Scott, C., Fong, J.H., Geer, L.Y., Geer, R.C., Gonzales, N.R., others, 2010. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic acids research 39, D225–D229.
Matsubayashi, Y., Sakagami, Y., 1996. Phytosulfokine, sulfated peptides that induce the proliferation of single mesophyll cells of Asparagus officinalis L. Proceedings of the National Academy of Sciences 93, 7623–7627.
Meyer, M., Huttenlocher, F., Cedzich, A., Procopio, S., Stroeder, J., Pau-Roblot, C., Lequart-Pillon, M., Pelloux, J., Stintzi, A., Schaller, A., 2016. The subtilisin-like protease SBT3 contributes to insect resistance in tomato. Journal of Experimental Botany 67, 4325–4338.
Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., Von Haeseler, A., Lanfear, R., 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular biology and evolution 37, 1530–1534.
Mirmostafaee, S., Azizi, M., Fujii, Y., 2020. Study of allelopathic interaction of essential oils from medicinal and aromatic plants on seed germination and seedling growth of lettuce. Agronomy 10, 163.
Neuteboom, L.W., Ng, J.M., Kuyper, M., Clijdesdale, O.R., Hooykaas, P.J., Van Der Zaal, B.J., 1999. Isolation and characterization of cDNA clones corresponding with mRNAs that accumulate during auxin-induced lateral root formation. Plant molecular biology 39, 273–287.
Norero, N.S., Castellote, M.A., de la Canal, L., Feingold, S.E., 2016. Genome-wide analyses of subtilisin-like serine proteases on Solanum tuberosum. American journal of potato research 93, 485–496.
Pearce, G., Yamaguchi, Y., Barona, G., Ryan, C.A., 2010. A subtilisin-like protein from soybean contains an embedded, cryptic signal that activates defense-related genes. Proceedings of the National Academy of Sciences 107, 14921–14925.
Potter, S.C., Luciani, A., Eddy, S.R., Park, Y., Lopez, R., Finn, R.D., 2018. HMMER web server: 2018 update. Nucleic acids research 46, W200–W204.
Preisigmuller, R., Gnau, P., Kindl, H., 1995. The inducible 9, 10-dihydrophenanthrene pathway: characterization and expression of bibenzyl synthase and S-adenosylhomocysteine hydrolase. Archives of biochemistry and biophysics 317, 201–207.
Raju, D., Schonauer, S., Hamzeh, H., Flynn, K.C., Bradke, F., Vom Dorp, K., Dörmann, P., Yildiz, Y., Trötschel, C., Poetsch, A., others, 2015. Accumulation of glucosylceramide in the absence of the beta-glucosidase GBA2 alters cytoskeletal dynamics. PLoS genetics 11, e1005063.
Ramírez, V., López, A., Mauch-Mani, B., Gil, M.J., Vera, P., 2013. An extracellular subtilase switch for immune priming in Arabidopsis. PLoS Pathogens 9, e1003445.
Rautengarten, C., Steinhauser, D., Büssis, D., Stintzi, A., Schaller, A., Kopka, J., Altmann, T., 2005. Inferring hypotheses on functional relationships of genes: analysis of the Arabidopsis thaliana subtilase gene family. PLoS Computational Biology 1, e40.
Rautengarten, C., Usadel, B., Neumetzler, L., Hartmann, J., Büssis, D., Altmann, T., 2008. A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats. The Plant Journal 54, 466–480.
Rawlings, N., Barrett, A., Bateman, A., 2010. MEROPS: the peptidase database. Nucleic 656 Acids Res. 38. D227–D233 657.
Redon, C., Pilch, D., Rogakou, E., Sedelnikova, O., Newrock, K., Bonner, W., 2002. Histone H2a variants H2AX and H2AZ. Current opinion in genetics & development 12, 162–169.
Reinecke, T., Kindl, H., 1993. Characterization of bibenzyl synthase catalysing the biosynthesis of phytoalexins of orchids. Phytochemistry 35, 63–66.
Riggs, C.D., Zeman, K., DeGuzman, R., Rzepczyk, A., Taylor, A.A., 2001. Antisense inhibition of a tomato meiotic proteinase suggests functional redundancy of proteinases during microsporogenesis. Genome 44, 644–650.
Roberts, I.N., Caputo, C., Kade, M., Criado, M., Barneix, A.J., 2011. Subtilisin-like serine proteases involved in N remobilization during grain filling in wheat. Acta Physiologiae Plantarum 33, 1997–2001.
Rose, R., Schaller, A., Ottmann, C., 2010. Structural features of plant subtilases. Plant signaling & behavior 5, 180–183.
Schaller, A., Stintzi, A., Graff, L., 2012. Subtilases–versatile tools for protein turnover, plant development, and interactions with the environment. Physiologia Plantarum 145, 52–66.
Schanz, S., Schröder, G., Schröder, J., 1992. Stilbene synthase from Scots pine (Pinus sylvestris). FEBS letters 313, 71–74.
Schonauer, S., Körschen, H.G., Penno, A., Rennhack, A., Breiden, B., Sandhoff, K., Gutbrod, K., Dörmann, P., Raju, D.N., Haberkant, P., others, 2017. Identification of a feedback loop involving β-glucosidase 2 and its product sphingosine sheds light on the molecular mechanisms in Gaucher disease. Journal of Biological Chemistry 292, 6177–6189.
Serrano, I., Buscaill, P., Audran, C., Pouzet, C., Jauneau, A., Rivas, S., 2016. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana. Elife 5, e19755.
Siezen, R.J., Leunissen, J.A., 1997. Subtilases: the superfamily of subtilisin-like serine proteases. Protein science 6, 501–523.
Sigrist, C.J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., Bucher, P., 2002. PROSITE: a documented database using patterns and profiles as motif descriptors. Briefings in bioinformatics 3, 265–274.
Stelpflug, S.C., Sekhon, R.S., Vaillancourt, B., Hirsch, C.N., Buell, C.R., de Leon, N., Kaeppler, S.M., 2016. An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development. The plant genome 9, plantgenome2015-04.
Subramanian, B., Gao, S., Lercher, M.J., Hu, S., Chen, W.-H., 2019. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic acids research 47, W270–W275.
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., others, 2015. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic acids research 43, D447–D452.
Tian, M., Huitema, E., Da Cunha, L., Torto-Alalibo, T., Kamoun, S., 2004. A Kazal-like extracellular serine protease inhibitor from Phytophthora infestans targets the tomato pathogenesis-related protease P69B. Journal of Biological Chemistry 279, 26370–26377.
Tornero, P., Conejero, V., Vera, P., 1997. Identification of a new pathogen-induced member of the subtilisin-like processing protease family from plants. Journal of Biological Chemistry 272, 14412–14419.
Tripathi, L.P., Sowdhamini, R., 2006. Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC genomics 7, 1–31.
Vartapetian, A., Tuzhikov, A., Chichkova, N., Taliansky, M., Wolpert, T., 2011. A plant alternative to animal caspases: subtilisin-like proteases. Cell Death & Differentiation 18, 1289–1297.
Veth-Tello, L.M., 2005. Analysis of gene expression in the outer cell layers of Arabidopsis roots during lateral root development (PhD Thesis). Leiden University.
Von Groll, U., Berger, D., Altmann, T., 2002. The subtilisin-like serine protease SDD1 mediates cell-to-cell signaling during Arabidopsis stomatal development. The Plant Cell 14, 1527–1539.
Voorrips, R., 2002. MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of heredity 93, 77–78.
Wang, L., Li, Y., Jin, X., Liu, L., Dai, X., Liu, Yanhui, Zhao, L., Zheng, P., Wang, X., Liu, Yeqiang, others, 2020. Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development. Communications biology 3, 1–15.
Wei, K., Chen, H., 2018. Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. BMC genomics 19, 1–18.
White, C.N., Proebsting, W.M., Hedden, P., Rivin, C.J., 2000. Gibberellins and seed development in maize. I. Evidence that gibberellin/abscisic acid balance governs germination versus maturation pathways. Plant Physiology 122, 1081–1088.
Yamaguchi, N., Winter, C.M., Wu, M.-F., Kanno, Y., Yamaguchi, A., Seo, M., Wagner, D., 2014. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science 344, 638–641.
Yamaguchi, Y., Barona, G., Ryan, C.A., Pearce, G., 2011. GmPep914, an eight-amino acid peptide isolated from soybean leaves, activates defense-related genes. Plant Physiology 156, 932–942.
Ylstra, B., Muskens, M., Van Tunen, A.J., 1996. Flavonols are not essential for fertilization in Arabidopsis thaliana. Plant molecular biology 32, 1155–1158.
Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., Ni, P., Dong, W., Hu, S., Zeng, C., others, 2005. The genomes of Oryza sativa: a history of duplications. PLoS biology 3, e38.
Zhao, C., Johnson, B.J., Kositsup, B., Beers, E.P., 2000. Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. Plant Physiology 123, 1185–1196.
Zimmermann, D., Gomez-Barrera, J.A., Pasule, C., Brack-Frick, U.B., Sieferer, E., Nicholson, T.M., Pfannstiel, J., Stintzi, A., Schaller, A., 2016. Cell death control by matrix metalloproteinases. Plant Physiology 171, 1456–1469.

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14 Jul, 2023
First submitted to journal
03 Jul, 2023

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Genome-Wide Identification and Characterization of the SBT Gene Family in maize and Its Expression in the Various tissue

Status:

Journal Publication

Version 1

Abstract

Figures

Introduction

Materials and methods

Materials

Sequence alignment and construction of a geophysical tree of ZmSBT

Gene structure, motif analysis and conservative domain analysis of ZmSBT

Chromosome distribution, gene duplication events and selection pressure analysis

Result

Identification and Characterization of Subtilisin-Like Serine Protease Genes in maize

Phylogenetic Analysis of maize SBTs

Gene Structure Characterization and protein Motif Identification

Chromosome location and evolutionary analyses of ZmSBTs

Cis-Acting Elements Identification in Promoter Region of ZmSBTs

Spatio-T emporal Expression Profiles of AcoSBTs in maize

Protein-Protein Networks Analysis of the ZmSBT Family Genes

Discussion

Conclusion

Declarations

References

Supplementary Tables

Additional Declarations

Supplementary Files

Status:

Journal Publication

Version 1