Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Miia Riitta Mäkelä, M. Di Falco, E. McDonnell, T.T.M. Nguyen, A. Wiebenga, Sari Kristiina Hilden, M. Peng, I.V. Grigoriev, A. Tsang, R.P. de Vries

Research output: Contribution to journalArticleScientificpeer-review

Abstract

We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.

Original languageEnglish
JournalStudies in Mycology
Issue number91
Pages (from-to)79-99
Number of pages21
ISSN0166-0616
DOIs
Publication statusPublished - Sep 2018
MoE publication typeA1 Journal article-refereed

Fields of Science

  • Aspergillus
  • Cellulose
  • Pectin
  • Plant biomass degradation
  • Wheat bran
  • Xylan
  • Xyloglucan
  • Sugar beet pulp
  • D-GALACTURONIC ACID
  • TRANSCRIPTIONAL ACTIVATOR
  • EXO-ARABINANASE
  • FUNGAL PATHOGEN
  • NIGER
  • REGULATOR
  • GENES
  • EXPRESSION
  • XLNR
  • CARBOHYDRATE
  • 1183 Plant biology, microbiology, virology

Cite this

Mäkelä, Miia Riitta ; Di Falco, M. ; McDonnell, E. ; Nguyen, T.T.M. ; Wiebenga, A. ; Hilden, Sari Kristiina ; Peng, M. ; Grigoriev, I.V. ; Tsang, A. ; de Vries, R.P. / Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. In: Studies in Mycology. 2018 ; No. 91. pp. 79-99.
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title = "Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli",
abstract = "We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.",
keywords = "Aspergillus, Cellulose, Pectin, Plant biomass degradation, Wheat bran, Xylan, Xyloglucan, Sugar beet pulp, D-GALACTURONIC ACID, TRANSCRIPTIONAL ACTIVATOR, EXO-ARABINANASE, FUNGAL PATHOGEN, NIGER, REGULATOR, GENES, EXPRESSION, XLNR, CARBOHYDRATE, 1183 Plant biology, microbiology, virology",
author = "M{\"a}kel{\"a}, {Miia Riitta} and {Di Falco}, M. and E. McDonnell and T.T.M. Nguyen and A. Wiebenga and Hilden, {Sari Kristiina} and M. Peng and I.V. Grigoriev and A. Tsang and {de Vries}, R.P.",
year = "2018",
month = "9",
doi = "10.1016/j.simyco.2018.09.001",
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Mäkelä, MR, Di Falco, M, McDonnell, E, Nguyen, TTM, Wiebenga, A, Hilden, SK, Peng, M, Grigoriev, IV, Tsang, A & de Vries, RP 2018, 'Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli', Studies in Mycology, no. 91, pp. 79-99. https://doi.org/10.1016/j.simyco.2018.09.001

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. / Mäkelä, Miia Riitta; Di Falco, M.; McDonnell, E.; Nguyen, T.T.M.; Wiebenga, A.; Hilden, Sari Kristiina; Peng, M.; Grigoriev, I.V.; Tsang, A.; de Vries, R.P.

In: Studies in Mycology, No. 91, 09.2018, p. 79-99.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

AU - Mäkelä, Miia Riitta

AU - Di Falco, M.

AU - McDonnell, E.

AU - Nguyen, T.T.M.

AU - Wiebenga, A.

AU - Hilden, Sari Kristiina

AU - Peng, M.

AU - Grigoriev, I.V.

AU - Tsang, A.

AU - de Vries, R.P.

PY - 2018/9

Y1 - 2018/9

N2 - We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.

AB - We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.

KW - Aspergillus

KW - Cellulose

KW - Pectin

KW - Plant biomass degradation

KW - Wheat bran

KW - Xylan

KW - Xyloglucan

KW - Sugar beet pulp

KW - D-GALACTURONIC ACID

KW - TRANSCRIPTIONAL ACTIVATOR

KW - EXO-ARABINANASE

KW - FUNGAL PATHOGEN

KW - NIGER

KW - REGULATOR

KW - GENES

KW - EXPRESSION

KW - XLNR

KW - CARBOHYDRATE

KW - 1183 Plant biology, microbiology, virology

U2 - 10.1016/j.simyco.2018.09.001

DO - 10.1016/j.simyco.2018.09.001

M3 - Article

SP - 79

EP - 99

JO - Studies in Mycology

JF - Studies in Mycology

SN - 0166-0616

IS - 91

ER -