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Review
. 2017 Aug 29:8:1602.
doi: 10.3389/fmicb.2017.01602. eCollection 2017.

Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

Vivek Sharma  1 , Richa Salwan  2 , P N Sharma  1 , Arvind Gulati  3
Affiliations
Review

Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

Vivek Sharma et al. Front Microbiol. .

Abstract

Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different "omics" approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.

Keywords: active mRNA; integrated omic; regulation; transcripts; translatome.

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Figures

FIGURE 1
FIGURE 1
Schematic flow of genetic information from genome to proteome level. A- Relationship of different omic approaches in Trichoderma–plant–plant pathogen interaction. B- Hierarchal relationship of total gene predicted using stacked ven diagram in the genome to the total mRNA transcribed (transcriptome) representing both stable and highly active mRNAs population under a stress response. Here depending upon the conditions and alternate splicing a > b > c > d or a > b > c = d or rarely a >b = c=d; a > b = c < d.
FIGURE 2
FIGURE 2
Pictorial representation of total mRNA transcripts, active mRNA involved in protein and bioactive metabolites synthesis during interaction with plant or plant pathogens. The figure explains that transcriptome based study in general represents a higher level of mRNA, compared to total translatome which represents only ribosomal loaded active mRNAs during interaction.
FIGURE 3
FIGURE 3
The experimental procedure of transcriptome and translatome for genome wide studies. In translatome ribosomal loaded or protected fragments of RNA are size or affinity fractionated, recovered, and ligated to adaptors for reverse transcription, amplification, and high-throughput RNA-seq whereas in transcriptome complete mRNA is used for subsequent analysis.
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