Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures

Lichtenberg, Jens; Keppler, Brian D.; Conley, Thomas; Gu, Dazhang; Burns, Peter D.; Welch, Lonnie R.; Showalter, Allan M.

doi:10.4236/ns.2012.412a141

Cited by 4 publications

(8 citation statements)

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“…The Bio OHIO 2.0 software program provides an efficient and reliable tool to identify proteins with biased amino acid compositions and known repetitive motifs [ 2 , 28 ]. The newly revised and improved 2.0 version integrated more functional modules that include searching for the presence of a signal peptide, GPI anchor, as well as automated BLAST searches against the Arabidopsis proteome.…”

Section: Discussionmentioning

confidence: 99%

“…tuberosum ) were downloaded from the Phytozome website ( www.phytozome.org ). The protein database was searched for EXTs using BIO OHIO 2.0 software, which integrated more functional modules into the software compared to BIO OHIO 1.0 [ 2 , 28 ]. Briefly, a regular expression of two or more SPPP repeats was used to search for candidate EXTs.…”

Section: Methodsmentioning

confidence: 99%

“…BIO OHIO 2.0 is a newly revised and improved bioinformatics software program developed at Ohio University that was tailored to fulfill this task [ 2 , 28 ]. The program was designed and developed for protein identification based on amino acid signatures, such as biased amino acid composition and common HRGP amino acid motifs in the genome-encoded protein sequences (i.e., the predicted proteome).…”

Section: Introductionmentioning

confidence: 99%

“…The program can also further analyze identified proteins by checking for the presence of potential signal peptide sequences and GPI anchor addition sequences and finding similar HRGPs via the Basic Local Alignment Search Tool (BLAST). Using this bioinformatics tool, Showalter et al [ 2 ] identified and classified the HRGP superfamily in Arabidopsis ( Arabidopsis thaliana ) and poplar ( Populus trichocarpa ), two fully sequenced plant genomes ([ 2 , 28 ]; Showalter et al, unpublished).…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom

et al. 2016

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Extensins (EXTs) are a family of plant cell wall hydroxyproline-rich glycoproteins (HRGPs) that are implicated to play important roles in plant growth, development, and defense. Structurally, EXTs are characterized by the repeated occurrence of serine (Ser) followed by three to five prolines (Pro) residues, which are hydroxylated as hydroxyproline (Hyp) and glycosylated. Some EXTs have Tyrosine (Tyr)-X-Tyr (where X can be any amino acid) motifs that are responsible for intramolecular or intermolecular cross-linkings. EXTs can be divided into several classes: classical EXTs, short EXTs, leucine-rich repeat extensins (LRXs), proline-rich extensin-like receptor kinases (PERKs), formin-homolog EXTs (FH EXTs), chimeric EXTs, and long chimeric EXTs. To guide future research on the EXTs and understand evolutionary history of EXTs in the plant kingdom, a bioinformatics study was conducted to identify and classify EXTs from 16 fully sequenced plant genomes, including Ostreococcus lucimarinus, Chlamydomonas reinhardtii, Volvox carteri, Klebsormidium flaccidum, Physcomitrella patens, Selaginella moellendorffii, Pinus taeda, Picea abies, Brachypodium distachyon, Zea mays, Oryza sativa, Glycine max, Medicago truncatula, Brassica rapa, Solanum lycopersicum, and Solanum tuberosum, to supplement data previously obtained from Arabidopsis thaliana and Populus trichocarpa. A total of 758 EXTs were newly identified, including 87 classical EXTs, 97 short EXTs, 61 LRXs, 75 PERKs, 54 FH EXTs, 38 long chimeric EXTs, and 346 other chimeric EXTs. Several notable findings were made: (1) classical EXTs were likely derived after the terrestrialization of plants; (2) LRXs, PERKs, and FHs were derived earlier than classical EXTs; (3) monocots have few classical EXTs; (4) Eudicots have the greatest number of classical EXTs and Tyr-X-Tyr cross-linking motifs are predominantly in classical EXTs; (5) green algae have no classical EXTs but have a number of long chimeric EXTs that are absent in embryophytes. Furthermore, phylogenetic analysis was conducted of LRXs, PERKs and FH EXTs, which shed light on the evolution of three EXT classes.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom

et al. 2016

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“…The Populus trichocarpa protein database (Ptrichocarpa_210_v3.0.protein.fa.gz) was downloaded from the Phytozome v11.0 website ( www.phytozome.org ) [ 21 ]. The protein database was searched for AGPs, EXTs, and PRPs using the newly revised and improved BIO OHIO 2.0 software [ 16 , 22 ]. Compared to the previous version, this new version integrated more functional modules that include searching for the presence of a signal peptide at the SignalP server ( www.cbs.dtu.dk/services/SignalP/ ) [ 23 ], searching for the presence of GPI anchor addition sequences using the big-PI plant predictor (mendel.imp.ac.at/gpi/plant_server.html) [ 24 ], as well as an automated BLAST search against Arabidopsis proteome.…”

Section: Methodsmentioning

confidence: 99%

Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa

et al. 2016

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BackgroundHydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa). This bioinformatics approach is based on searching for biased amino acid compositions and for particular protein motifs associated with known HRGPs with a newly revised and improved BIO OHIO 2.0 program. Proteins detected by the program are subsequently analyzed to identify the following: 1) repeating amino acid sequences, 2) signal peptide sequences, 3) glycosylphosphatidylinositol lipid anchor addition sequences, and 4) similar HRGPs using the Basic Local Alignment Search Tool (BLAST).ResultsThe program was used to identify and classify 271 HRGPs from poplar including 162 AGPs, 60 EXTs, and 49 PRPs, which are each divided into various classes. This is in contrast to a previous analysis of the Arabidopsis proteome which identified 162 HRGPs consisting of 85 AGPs, 59 EXTs, and 18 PRPs. Poplar was observed to have fewer classical EXTs, to have more fasciclin-like AGPs, plastocyanin AGPs and AG peptides, and to contain a novel class of PRPs referred to as the proline-rich peptides.ConclusionsThe newly revised and improved BIO OHIO 2.0 bioinformatics program was used to identify and classify the inventory of HRGPs in poplar in order to facilitate and guide basic and applied research on plant cell walls. The newly identified poplar HRGPs can now be examined to determine their respective structural and functional roles, including their possible applications in the areas plant biofuel and natural products for medicinal or industrial uses. Additionally, other plants whose genomes are sequenced can now be examined in a similar way using this bioinformatics program which will provide insight to the evolution of the HRGP family in the plant kingdom.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0912-3) contains supplementary material, which is available to authorized users.

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In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development

et al. 2019

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Key messageThe fasciclin-like arabinogalactan proteins organization into four groups is conserved and may be related to specific roles in developmental processes across angiosperms.AbstractFasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs), which contain fasciclin-like domains in addition to typical AGP domains. FLAs are present across all embryophytes, and despite their low overall sequence similarity, conserved regions that define the fasciclin functional domain (FAS) have been identified, suggesting that the cell adhesion property is also conserved. FLAs in Arabidopsis have been organized into four subgroups according to the number and distribution of functional domains. Recent studies associated FLAs with cell wall-related processes where domain organization seemed to be related to functional roles. In Arabidopsis, FLAs containing a single FAS domain were found to be important for the integrity and elasticity of the plant cell wall matrix, and FLAs with two FAS domains and two AGP domains were found to be involved in maintaining proper cell expansion under salt stress conditions. The main purpose of the present work was to elucidate the expression pattern of selected FLA genes during embryo and seed development using RT-qPCR. AtFLA8 and AtFLA10, two Arabidopsis genes that stood out in previous microarray studies of embryo development, were further examined using promoter-driven gene reporter analyses. We also studied the expression of cork oak FLA genes and found that their expression partially parallels the expression patterns of the putative AtFLA orthologs. We propose that the functional organization of FLAs is conserved and may be related to fundamental aspects of embryogenesis and seed development across angiosperms. Phylogenetic studies were performed, and we show that the same basic four-subgroup organization described for Arabidopsis FLA gene classification is valid for most Arabidopsis FLA orthologs of several plant species, namely poplar, corn and cork oak.Electronic supplementary materialThe online version of this article (10.1007/s00497-019-00376-7) contains supplementary material, which is available to authorized users.

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Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures

Cited by 4 publications

References 12 publications

Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom

Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom

Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa

In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development

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