Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics.

Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.

Revision on the Genus Paris in Thailand, with a New Species Paris siamensis.

The genus Paris is an important and confusing taxon due to high variation within species, and differences between species are sometimes difficult to delimit. Thus, the status of some taxa has changed over time. To clarify the status of Paris species for plant conservation and effective management of this genus in Thailand, we performed an intensive survey in northern Thailand, studied morphological characteristics, and constructed a molecular phylogenic tree, which we compared to recently published results of this genus. Our results indicate that there are two species in Thailand: P. yunnanensis and a new species, P. siamensis. Detailed descriptions, illustrations, and the phylogenetic position of these two species are provided here.

Application of Hierarchical Clustering to Analyze Solvent-Accessible Surface Area Patterns in Amycolatopsis lipases.

The wealth of biological databases provides a valuable asset to understand evolution at a molecular level. This research presents the machine learning approach, an unsupervised agglomerative hierarchical clustering analysis of invariant solvent accessible surface areas and conserved structural features of Amycolatopsis eburnea lipases to exploit the enzyme stability and evolution. Amycolatopsis eburnea lipase sequences were retrieved from biological database. Six structural conserved regions and their residues were identified. Total Solvent Accessible Surface Area (SASA) and structural conserved-SASA with unsupervised agglomerative hierarchical algorithm were clustered lipases in three distinct groups (99/96%). The minimum SASA of nucleus residues was related to Lipase-4. It is clearly shown that the overall side chain of SASA was higher than the backbone in all enzymes. The SASA pattern of conserved regions clearly showed the evolutionary conservation areas that stabilized Amycolatopsis eburnea lipase structures. This research can bring new insight in protein design based on structurally conserved SASA in lipases with the help of a machine learning approach.

Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins.

A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.

Gelatinization, pasting and retrogradation properties and molecular fine structure of starches from seven cassava cultivars.

Genetic diversity in the physicochemical properties and fine structures of seven cassava starches samples was studied. The apparent amylose content ranged from 24.8 to 27.6%. The whole branched starches showed significant differences in average hydrodynamic radius, ranging from 53.35 to 58.45 nm, while debranched starch exhibited differences in degrees of polymerization and height of both amylose and amylopectin peaks. The molecular size of amylose and amylopectin was positively correlated. The amount of short chains fa (6 ≤ X ≤ 12) and fb1 (13 ≤ X ≤ 24) had significant differences among the cultivars. Structure-function relation analysis indicated that the CPV and SB were mainly determined by amylopectin fine structures, BD, PTi and Tp and retrogradation properties were mainly determined by the amylose fine structure, while PTe and To were mainly affected by both amylose and amylopectin fine structures. The current findings will be helpful to improve the understanding cassava starch quality for use in industrial starch applications.

Rheological characteristics and genotype correlation of cassava root for very high gravity ethanol production: The influence of cassava varieties and harvest times.

In very high gravity (VHG) ethanol fermentation, the rheological properties of native cassava significantly influence heat and mass transfer, mixing energy, and, thus, the yield of all steps. This study investigated the effect of cassava varieties and their harvest times on starch liquefaction, saccharification, and fermentation. The genotype correlation of the starch properties was revealed for the most suitable cassava varieties. First, the starch content, amylose content, total reducing sugar from liquefaction and saccharification, pasting properties, and ethanol yields of six cassava varieties (Huay Bong 60, Hanatee, Kasetsart 50, Pirun 1, Pirun 2, and Rayong 11) at 6-, 9-, 12-, and 15-month harvest times were evaluated. The amylose content increased significantly from the 6th to the 12th month but slightly decreased at the 15th month. It was observed that the starch content contributed to a more substantial influence on the change in peak viscosity than on the amylose content. Ethanol fermentation using Saccharomyces cerevisiae TISTR5606 showed that the Rayong 11 variety at the 15-month harvest time provided the highest ethanol concentration of 104.7 ± 4.1 g L-1 and an ethanol yield of 0.4 ± 0.1 g ethanol g-1 reducing sugar, which corresponded to 74.5% of the theoretical yield.

Identification and expression of genes in response to cassava bacterial blight infection.

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (or XAM) is a serious disease of cassava (Manihot esculenta Crantz). In this study, quantitative trait loci (QTL) associated with CBB infection were identified in the F1 progenies of a cross between the "Huay Bong 60" and "Hanatee" cassava cultivars. The phenotype of disease severity was observed at 7, 10, and 12 days after inoculation (DAI). A total of 12 QTL were identified, of which 5, 6, and 1 were detected in 7, 10, and 12 DAI samples, respectively. Among all identified QTL, CBB14_10dai_1, CBB14_10dai_2, and CBB14_12dai showed the most significant (P < 0.0001) associations with CBB infection, and explained 21.3, 13.8, and 26.5% of phenotypic variation, respectively. Genes underlying the QTL were identified and their expression was investigated in resistant and susceptible cassava plants by real-time quantitative RT-PCR. The results identified candidate genes that showed significant differences in expression between resistant and susceptible lines, including brassinosteroid insensitive 1-associated receptor kinase 1-related (Manes.04G059100), cyclic nucleotide-gated ion channel 2 (Manes.02G051100), and autophagy-related protein 8a-related (Manes.17G026600) at 7 DAI, and regulator of nonsense transcripts 1 homolog (Manes.17G021900) at both 7 and 12 DAI. The expression pattern of all genes showed higher levels in resistant (B82, B32, B20, and B70) as compared to susceptible (HB60, B100, B95, and B47) plants. Overall, this study has identified QTL and markers linked to CBB infection trait, and identified candidate genes involved in CBB resistance. This information will be of use for better understanding defense mechanisms in cassava to bacterial blight disease.

Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray.

Cassava anthracnose disease (CAD), caused by the fungus Colletotrichum gloeosporioides f. sp. Manihotis, is a serious disease of cassava (Manihot esculenta) worldwide. In this study, we established a cassava oligonucleotide-DNA microarray representing 59,079 probes corresponding to approximately 30,000 genes based on original expressed sequence tags and RNA-seq information from cassava, and applied it to investigate the molecular mechanisms of resistance to fungal infection using two cassava cultivars, Huay Bong 60 (HB60, resistant to CAD) and Hanatee (HN, sensitive to CAD). Based on quantitative real-time reverse transcription PCR and expression profiling by the microarray, we showed that the expressions of various plant defense-related genes, such as pathogenesis-related (PR) genes, cell wall-related genes, detoxification enzyme, genes related to the response to bacterium, mitogen-activated protein kinase (MAPK), genes related to salicylic acid, jasmonic acid and ethylene pathways were higher in HB60 compared with HN. Our results indicated that the induction of PR genes in HB60 by fungal infection and the higher expressions of defense response-related genes in HB60 compared with HN are likely responsible for the fungal resistance in HB60. We also showed that the use of our cassava oligo microarray could improve our understanding of cassava molecular mechanisms related to environmental responses and development, and advance the molecular breeding of useful cassava plants.

Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map.

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ∼4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection.

SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz).

Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.