fungi such as Geotrichum candidum, Botrytis cinerea, Pleurotus eryngii, Pleurotus
sajor-caju, Pleurotus pulmonarius, Penicillium simplicissimum, Phanerochaete
chrysosporium, Brachypsectra fulva, Fusarium solani, Bjerkandera adusta, and
Rigidoporus microporus, and one bacterium Sphingobacterium sp. ATM is reported
to exhibit this enzyme. Few Pseudomonas sp. under anaerobic conditions also show
the presence of veratryl alcohol oxidase analog. This enzyme can efficiently modify
or degrade aromatic alcohols produced during the degradation of lignin.
4.6
Role of Genomics and Proteomics in Understanding Lignin
Degradation
Introduction of new molecular techniques in genomics, transcriptomics, and proteomics and advances in instrumental resolution paved the way for improved understanding of lignocellulosic biomass deconstruction by individual microbes and
complex microbial communities. The increasingly available genomic data for bacteria and fungi indicate the potential of microbes for biomass degradation across
diverse taxa. Comparative analysis of genome gives information regarding their
taxonomic classification and possible physiological prospective (Baldrian and
López-Mondéjar 2014). Recent development in NGS applied on lignocellulosedegrading fungi, bacteria, and complex community has been reviewed (Kameshwar
and Qin 2016). The genome sequence of individual bacterial strain of actinobacteria,
α-proteobacteria, β-proteobacteria, and γ-proteobacteria along with their important
genomic features responsible for lignin degradation has been reported (Kameshwar
and Qin 2016). Improvement in liquid chromatography and mass spectrometry with
quantitative proteomics techniques such as isobaric tags for relative and absolute
quantitation (iTRAQ) and label-free quantification (LFQ) has provided a solid
platform to quantify proteins and their expression studies.
Enzyme production study at different time points can be performed to study the
set of proteins expressed at a specified time under different culture conditions
(Baldrian and López-Mondéjar 2014; Singh et al. 2017). Novel ligninolytic enzymes
and unannotated proteins responsible for degradation can be identified. In recent
studies, NGS is complemented with proteomics and metabolomics to get further
precise information regarding pattern of bacterial biomass degradation. The genome
sequence of some of the recently reported lignin-degrading bacteria are Tolumonas
lignilytica, Pandoraea sp. ISTKB, Pseudomonas sp. strain YS-1p, Rhizobium sp.
strain YS-1r, and Burkholderia sp. strain LIG30 (Woo et al. 2014; Billings et al.
2015; Prabhakaran et al. 2015; Bao et al. 2015; Kumar et al. 2016). Kumar et al.
(2018) recently reported genomics and proteomics for understanding the novel
genes, differential expression of the important genes on Kraft lignin and vanillic
acid (most common intermediate found during lignin degradation). Novel pathways
and enzymes were discovered for phenylacetate and benzoate (Kumar et al. 2018).
Lin et al. (2016) used proteomics and genomics approach and engineered Pseudomonas sp. A514 for efficient lignin utilization and bioconversion. The
polyhydroxyalkanoate production efficiency reached 73% of bacterial cell dry
4 Bacterial-Mediated Depolymerization and Degradation of Lignin
99
sajor-caju, Pleurotus pulmonarius, Penicillium simplicissimum, Phanerochaete
chrysosporium, Brachypsectra fulva, Fusarium solani, Bjerkandera adusta, and
Rigidoporus microporus, and one bacterium Sphingobacterium sp. ATM is reported
to exhibit this enzyme. Few Pseudomonas sp. under anaerobic conditions also show
the presence of veratryl alcohol oxidase analog. This enzyme can efficiently modify
or degrade aromatic alcohols produced during the degradation of lignin.
4.6
Role of Genomics and Proteomics in Understanding Lignin
Degradation
Introduction of new molecular techniques in genomics, transcriptomics, and proteomics and advances in instrumental resolution paved the way for improved understanding of lignocellulosic biomass deconstruction by individual microbes and
complex microbial communities. The increasingly available genomic data for bacteria and fungi indicate the potential of microbes for biomass degradation across
diverse taxa. Comparative analysis of genome gives information regarding their
taxonomic classification and possible physiological prospective (Baldrian and
López-Mondéjar 2014). Recent development in NGS applied on lignocellulosedegrading fungi, bacteria, and complex community has been reviewed (Kameshwar
and Qin 2016). The genome sequence of individual bacterial strain of actinobacteria,
α-proteobacteria, β-proteobacteria, and γ-proteobacteria along with their important
genomic features responsible for lignin degradation has been reported (Kameshwar
and Qin 2016). Improvement in liquid chromatography and mass spectrometry with
quantitative proteomics techniques such as isobaric tags for relative and absolute
quantitation (iTRAQ) and label-free quantification (LFQ) has provided a solid
platform to quantify proteins and their expression studies.
Enzyme production study at different time points can be performed to study the
set of proteins expressed at a specified time under different culture conditions
(Baldrian and López-Mondéjar 2014; Singh et al. 2017). Novel ligninolytic enzymes
and unannotated proteins responsible for degradation can be identified. In recent
studies, NGS is complemented with proteomics and metabolomics to get further
precise information regarding pattern of bacterial biomass degradation. The genome
sequence of some of the recently reported lignin-degrading bacteria are Tolumonas
lignilytica, Pandoraea sp. ISTKB, Pseudomonas sp. strain YS-1p, Rhizobium sp.
strain YS-1r, and Burkholderia sp. strain LIG30 (Woo et al. 2014; Billings et al.
2015; Prabhakaran et al. 2015; Bao et al. 2015; Kumar et al. 2016). Kumar et al.
(2018) recently reported genomics and proteomics for understanding the novel
genes, differential expression of the important genes on Kraft lignin and vanillic
acid (most common intermediate found during lignin degradation). Novel pathways
and enzymes were discovered for phenylacetate and benzoate (Kumar et al. 2018).
Lin et al. (2016) used proteomics and genomics approach and engineered Pseudomonas sp. A514 for efficient lignin utilization and bioconversion. The
polyhydroxyalkanoate production efficiency reached 73% of bacterial cell dry
4 Bacterial-Mediated Depolymerization and Degradation of Lignin
99